Is vba an open source (or source availble) emulator? If it is, looking into the source code could shed some light on the modifications present in the vba4hanmaru version. You may also want to find a PC dissasembler and compare the results (using a tool such as diff), however, in that case, you'd only get useful information if the unmodified version you where comparing against was compiled with the same compiler as the modified one.
If you've located what appears to the patch, you can extract it using a tool that reads and writes binary data from within files. (On un*x, I'd suggest dd, but I don't know what to recommend on other platforms.) You could also extract it with a fairly easy to write program if you know how to code. In Python you could use something like this:
f1 = file('vba4hanmaru.exe', 'rb')
f2 = file('patch.ips', 'wb')
f1.seek(0xDEADBEEF) # Use the proper offset, of course.
data = f1.read(42) # Ditto for size.
f2.write(data)
What format does the patch appear to be in? Does it have a recognizable header? If it starts with "IPS", then it may have the "EOF" marker at the end which would tell you how much data to extract. (Although, the IPS standard isn't very standard, so it may not.)
I'm sure it can be done, so keep at it.